Plasmid DNA isolation (i.e., plasmid preps, mini-preps, rapid DNA preps, among other procedures) remains a necessary and arduous laboratory task. Plasmid DNA isolation from bacteria has traditionally been performed using the “alkaline lysis” method, in which resuspended bacteria are lysed in NaOH/SDS, neutralized in sodium acetate, and then subjected to centrifugation to remove cell debris (denatured proteins and genomic DNA). Plasmid DNA remains in suspension, ready for further processing (see, e.g., Sambrook and Russel, 2001).
Current popular methods of plasmid DNA preparation are based on the alkaline lysis method followed by separating the flocculent cell debris, including denatured genomic DNA from the plasmid DNA, using a spin-column. The plasmid DNA is typically recovered in a centrifuge tube component of the spin-column, while bacterial debris remains in a lysate filtration device, which is eventually removed and discarded. The recovered DNA must be further transferred and manipulated to remove salts or other contaminants.
While the use of popular spin-column lysate filtration devices has improved the speed and efficiency of plasmid preparation, current methods and apparatus continue to require the separate and sequential addition of the conventional alkaline lysis reagents, i.e., cell pellet resuspension reagent (P1), lysis buffer (P2), and neutralization buffer (P3). Even if bacterial media can be used directly, as in the case of high copy number plasmids, P2 and P3 must still be separately and sequentially added to the cell suspension.
Current methods also require transferring the final cell suspension from a centrifuge tube (or other container in which the bacteria and reagents were combined), to a separate spin-column filtration apparatus, then further transferring and manipulating the filtered lysate to remove contaminants. Current methods are particularly time consuming, tedious, and inefficient (in terms of recovery) when applied to large-scale plasmid DNA preparations.